Three years ago, I came across the victims of a drone strike about an hour after it occurred. It was in Gaza – although the location for the purposes of this piece does not matter; only the fact of the weapons system. The drone had fired a missile at a militant commander. Standing close by at that moment was a group of children waiting for a lift to school, three of whom were wounded.

All injury and death is horrible, that suffered by innocents doubly so. Having seen so much of the human consequences of war, I tend not to distinguish which weapon has been responsible but try to see the intent behind the attack that caused the injury and death. In conflict, within the existing framework of international humanitarian law, whether an attack is justifiable and legal is defined both by the nature of the target and proper consideration of whether there will be civilian casualties and whether they are avoidable.

For this reason, I find the notion of drone warfare no more horrible than a Tomahawk cruise missile fired from a distant ship or a bomb dropped indiscriminately on a village by a high-flying F-22 or MiG. What did bother me about that drone strike three years ago – about all drone strikes that cause civilian injuries and death – was the knowledge that, unlike a jet pilot or artilleryman firing a shell on to co-ordinates where he cannot see who is nearby, this aircraft's remote pilot must have been able to see the children who would be injured.

The use of drones to conduct lethal strikes, particularly by the US and often causing civilian casualties, has come to be one of the most deeply controversial moral issues in the development of modern conflict, driven by the fourfold escalation in the use of drones by President Barack Obama in the global "war on terror" from Pakistan and Afghanistan to Yemen and Somalia. The most recent incident occurred yesterday in northern Pakistan – the first in over a month – when five alleged militants were killed in a drone strike on the compound of a local warlord. So controversial indeed is the subject that last month Congress indicated it was seeking the internal White House memos used to authorise drone strikes where US citizens fighting with militants had been killed. The UK, too, has been drawn in through a court case brought by a Pakistani student demanding to know whether this country has provided intelligence for a suspected US drone strike that killed his father.

Despite genuine concerns over drone warfare, much of what has been written on both sides of the debate on the surrounding moral and legal issues has been ill-informed and confused. In part, this is because for some the issue has become conflated with broader geopolitical concerns, not least a critique of US military power. While how we understand the use of military power by a state should serve as an important context, it does not assist in understanding whether the use of drones is legitimate.

For many, the nature of drone warfare itself has become central. The operators' very remoteness, it is claimed, leads to desensitisation. But throughout the history of weapons, designers have always sought to maximise lethality while reducing the vulnerability of those using the weapons. And while it has long been accepted that there is a relationship between increased distance from a target and the ability to kill with reduced feelings of guilt, recent anecdotal evidence suggests that some drone operators, because they spend so long intimately observing their targets, experience the same emotional damage as those who kill at close quarters.

What then of the issue of international legality? As Joshua Foust and Ashley Boyle argue in a new paper, The Strategic Context of Lethal Drones for the American Security Project, this, too, is more complex than some have assumed. The use of force against countries in peacetime, as they point out, is governed by Article 51 of the UN Charter. This permits "the right of individual or collective defence" across borders in peacetime if either one of two requirements is satisfied: that the group or individuals being targeted poses a threat or if the country, where the strike takes place, "consents". While Pakistan has complained that drone strikes "infringe its sovereignty", strong evidence exists that suggests it is heavily involved in providing the intelligence and other participation for strikes.

A case can be made too that drones might be "more ethical" than other older systems because they can be more discriminate, lingering over their target for hours or returning for days to the location, giving those authorising the operations the opportunity to minimise noncombatant casualties.

Paradoxically, it is precisely because of this potential for discrimination, in the context of the execution of the US drone war, that their use has become more morally problematic because it brings us back to the subject of intent, not least in the way in which the US has drawn up its "kill lists" and in its definition of when civilian casualties are acceptable and how those casualties are counted. When Thomas Aquinas condoned killing in self-defence, he defined the moral "doctrine of double effect", a key concept in Just War theory from Francisco de Vitoria in the 16th century to Michael Walzer in the modern era.

In this context, it sets the killing of civilians, or the risk of killing them, as "a bad effect" against what might be viewed as moral within the bounds of self-defence. For while there are very few who would try to deny that a militant threat exists in areas where strikes take place, the central issue comes down to how those combatants are identified and what efforts are being made to protect civilians. One of the most shocking disclosures about the details of Obama's decision-making process is the use of the definition "militant" for all males of military age within a drone strike zone, regardless of whether they are combatants or not.

This definition is a deliberate evasion of the moral responsibility supposed to be built into the targeting process. Add to that the often wild vagaries of the US intelligence that nominates the list of those who pose an alleged threat, failures of which I witnessed on many occasions in Iraq, and it seems certain that there have been strikes, perhaps many, which have been unjustifiable in their civilian death toll.

If there is a final compelling question to be asked over the future of drone warfare, it is the one posed by Foust and Boyle who demanded whether, as a military tool, drone warfare is actually effective; whether its use is justified when set against the political fallout that the drone campaign has produced and whether drones have actually reduced the threat posed by militants.

Without clarity on these issues – that the drone campaign is operated within a real, clear and publicly defensible moral framework and serves a quantifiable defence purpose – the questions about drones will only get louder and more insistent.